Contacts of the helix formed by residues 1473 - 1486 (chain C) in PDB entry 5Y3R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR1473 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1470C SER* 2.8 22.1 + - - -
1472C SER* 1.3 89.3 + - - +
1474C ASP* 1.3 77.4 + - - +
1477C HIS* 2.8 45.0 + - + -
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Residues in contact with ASP1474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1470C SER 3.3 6.8 + - - +
1473C THR* 1.3 94.3 - - - +
1475C LEU* 1.3 65.7 + - + +
1477C HIS* 2.7 13.3 + - - +
1478C SER* 2.4 44.0 + - - +
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Residues in contact with LEU1475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1427C SER* 3.8 22.9 - - - -
1428C ILE* 5.1 13.2 - - + +
1431C LEU* 3.7 27.1 - - + +
1468C LEU* 4.0 8.3 - - + -
1470C SER 5.2 0.2 - - - +
1471C GLN* 3.2 61.9 + - + +
1474C ASP* 1.3 83.6 - - + +
1476C HIS* 1.3 66.8 + - + +
1478C SER* 3.1 4.6 + - - -
1479C VAL* 2.9 27.2 + - - +
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Residues in contact with HIS1476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1468C LEU* 3.3 33.6 - - + +
1471C GLN 3.1 12.3 + - - -
1472C SER* 2.8 31.4 + - - +
1473C THR 4.3 0.2 - - - +
1474C ASP 3.2 0.6 - - - -
1475C LEU* 1.3 76.7 - - + +
1477C HIS* 1.3 64.3 + - + +
1479C VAL* 3.2 6.5 - - - +
1480C GLY 3.6 1.7 + - - -
1506C SER 3.1 17.7 - - - -
1507C CYS* 2.2 64.3 + - - +
1509C GLN* 5.4 0.4 - - + -
1510C LEU* 3.7 21.5 - - + +
1511C ALA* 4.3 14.1 - - + -
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Residues in contact with HIS1477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472C SER 5.2 0.9 - - - -
1473C THR* 2.8 47.0 + - + +
1474C ASP* 2.7 18.1 + - - +
1476C HIS* 1.3 75.4 - - + +
1478C SER* 1.3 53.8 + - - +
1480C GLY* 2.4 35.4 + - - -
1481C THR* 2.9 5.3 + - - +
1511C ALA* 5.7 5.3 - - + +
1515C LEU* 4.6 27.9 - - + +
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Residues in contact with SER1478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428C ILE* 6.0 0.5 - - - +
1431C LEU* 4.1 27.1 - - - +
1474C ASP* 2.4 38.4 + - - +
1475C LEU* 3.1 5.9 + - - -
1477C HIS* 1.3 67.2 - - - +
1479C VAL* 1.3 55.8 + - - +
1481C THR* 2.6 36.6 + - - -
1482C GLU* 2.9 20.2 + - - +
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Residues in contact with VAL1479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431C LEU* 5.2 5.3 - - + +
1475C LEU 2.9 20.2 + - - +
1476C HIS* 3.2 9.9 - - - +
1478C SER* 1.3 74.5 - - - +
1480C GLY* 1.3 57.9 + - - +
1482C GLU* 4.2 9.6 + - - +
1483C LEU* 2.8 38.2 + - + +
1503C LEU* 3.2 40.4 - - + +
1504C ASP* 3.1 28.3 - - - +
1507C CYS* 3.4 19.7 - - + -
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Residues in contact with GLY1480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476C HIS 3.6 2.4 + - - -
1477C HIS 2.4 22.1 + - - -
1479C VAL* 1.3 67.8 - - - +
1481C THR* 1.3 49.2 + - - -
1482C GLU 3.0 2.0 - - - -
1483C LEU* 4.6 7.0 - - - -
1484C LEU* 2.3 42.2 + - - +
1507C CYS* 5.0 0.8 - - - -
1519C PHE* 4.2 13.5 - - - -
1563C PHE* 6.5 0.2 - - - -
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Residues in contact with THR1481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477C HIS* 2.9 4.8 + - - +
1478C SER* 2.6 34.4 + - - -
1480C GLY* 1.3 73.2 - - - +
1482C GLU* 1.3 52.7 - - + -
1484C LEU* 3.1 19.6 - - + +
1485C SER* 2.0 37.6 + - - +
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Residues in contact with GLU1482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1431C LEU* 3.1 49.5 - - - +
1432C CYS* 4.2 3.8 + - - -
1435C ASN* 3.2 29.3 + - + +
1478C SER* 2.9 20.1 + - - +
1479C VAL* 3.8 9.8 - - - +
1480C GLY 3.0 0.2 - - - -
1481C THR* 1.3 84.5 - - + +
1483C LEU* 1.3 62.0 + - - +
1484C LEU 2.9 0.7 - - - -
1485C SER* 2.3 27.4 + - - +
1486C LEU* 2.9 13.5 + - - +
1503C LEU* 4.4 16.6 - - + +
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Residues in contact with LEU1483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479C VAL* 2.8 21.9 + - + +
1480C GLY* 5.2 4.7 - - - -
1482C GLU* 1.3 71.9 - - - +
1484C LEU* 1.3 62.2 + - - +
1486C LEU* 3.9 13.3 + - + +
1500C LEU* 5.2 14.1 - - + +
1504C ASP* 3.7 31.4 - - - +
1508C LYS* 5.9 5.6 - - - +
1562C LEU* 4.2 6.5 - - + +
1563C PHE* 3.3 32.2 - - + -
1566C THR* 3.6 35.9 - - + +
1570C GLU* 4.6 10.8 - - + +
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Residues in contact with LEU1484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1480C GLY 2.3 37.0 + - - +
1481C THR* 3.1 24.9 - - + +
1483C LEU* 1.3 79.3 - - - +
1485C SER* 1.3 59.9 + - - +
1486C LEU 2.9 7.6 + - - -
1487C VAL* 3.6 20.1 + - + +
1488C TYR* 6.5 0.4 - - + -
1519C PHE* 3.4 33.9 - - + -
1523C GLY* 4.9 7.2 - - - +
1526C GLU* 6.5 0.9 - - + -
1562C LEU* 5.2 0.3 - - - +
1563C PHE* 4.0 16.8 - - + -
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Residues in contact with SER1485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435C ASN* 3.4 20.7 + - - -
1481C THR* 2.0 36.1 + - - +
1482C GLU* 2.3 22.6 + - - +
1484C LEU* 1.3 72.2 - - - +
1486C LEU* 1.3 60.5 + - - -
1487C VAL* 3.1 2.2 + - - +
1488C TYR* 3.1 39.0 + - - +
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Residues in contact with LEU1486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435C ASN* 5.2 4.2 - - - +
1482C GLU 2.9 10.9 + - - +
1483C LEU* 4.2 12.1 - - + +
1484C LEU 2.9 1.6 + - - -
1485C SER* 1.3 77.9 - - - +
1487C VAL* 1.3 50.9 + - - +
1489C LYS* 2.7 60.2 + - + +
1490C GLY 2.8 30.2 + - - +
1492C ALA* 3.5 32.1 - - + +
1493C PRO* 5.6 0.2 - - + -
1496C GLU* 5.0 7.9 - - + -
1497C ARG* 5.0 8.1 - - - +
1500C LEU* 5.5 9.2 - - + -
1557C GLU* 5.6 2.5 - - - +
1562C LEU* 5.8 9.4 - - + -
1565C GLU* 6.5 0.4 - - - -
1566C THR* 5.7 5.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il